phenoml 0.0.6__py3-none-any.whl

phenoml/construe/types/__init__.py

@@ -0,0 +1,41 @@
+# This file was auto-generated by Fern from our API Definition.
+
+# isort: skip_file
+
+from .bad_request_error_body import BadRequestErrorBody
+from .construe_cohort_request_config import ConstrueCohortRequestConfig
+from .construe_cohort_response import ConstrueCohortResponse
+from .construe_cohort_response_queries_item import ConstrueCohortResponseQueriesItem
+from .construe_cohort_response_queries_item_code_extract_results_item import (
+    ConstrueCohortResponseQueriesItemCodeExtractResultsItem,
+)
+from .construe_cohort_response_queries_item_code_extract_results_item_codes_item import (
+    ConstrueCohortResponseQueriesItemCodeExtractResultsItemCodesItem,
+)
+from .construe_upload_code_system_response import ConstrueUploadCodeSystemResponse
+from .extract_codes_result import ExtractCodesResult
+from .extract_request_config import ExtractRequestConfig
+from .extract_request_config_chunking_method import ExtractRequestConfigChunkingMethod
+from .extract_request_system import ExtractRequestSystem
+from .extracted_code_result import ExtractedCodeResult
+from .internal_server_error_body import InternalServerErrorBody
+from .unauthorized_error_body import UnauthorizedErrorBody
+from .upload_request_format import UploadRequestFormat
+
+__all__ = [
+    "BadRequestErrorBody",
+    "ConstrueCohortRequestConfig",
+    "ConstrueCohortResponse",
+    "ConstrueCohortResponseQueriesItem",
+    "ConstrueCohortResponseQueriesItemCodeExtractResultsItem",
+    "ConstrueCohortResponseQueriesItemCodeExtractResultsItemCodesItem",
+    "ConstrueUploadCodeSystemResponse",
+    "ExtractCodesResult",
+    "ExtractRequestConfig",
+    "ExtractRequestConfigChunkingMethod",
+    "ExtractRequestSystem",
+    "ExtractedCodeResult",
+    "InternalServerErrorBody",
+    "UnauthorizedErrorBody",
+    "UploadRequestFormat",
+]

phenoml/construe/types/bad_request_error_body.py

@@ -0,0 +1,27 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+
+
+class BadRequestErrorBody(UniversalBaseModel):
+    status: typing.Optional[int] = pydantic.Field(default=None)
+    """
+    HTTP status code.
+    """
+
+    message: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Error message.
+    """
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/construe/types/construe_cohort_request_config.py

@@ -0,0 +1,37 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+
+
+class ConstrueCohortRequestConfig(UniversalBaseModel):
+    include_extract_results: typing.Optional[bool] = pydantic.Field(default=None)
+    """
+    When enabled, includes detailed information about medical codes extracted from the text.
+    """
+
+    include_rationale: typing.Optional[bool] = pydantic.Field(default=None)
+    """
+    When enabled, includes AI-generated explanations for each query component and code extraction.
+    """
+
+    exclude_deceased: typing.Optional[bool] = pydantic.Field(default=None)
+    """
+    Controls whether deceased patients should be excluded from the cohort.
+    """
+
+    sql_syntax: typing.Optional[typing.Literal["bigquery"]] = pydantic.Field(default=None)
+    """
+    Specifies the SQL dialect for query generation. Currently, only "bigquery" is supported.
+    """
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/construe/types/construe_cohort_response.py

@@ -0,0 +1,33 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+import typing_extensions
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+from ...core.serialization import FieldMetadata
+from .construe_cohort_response_queries_item import ConstrueCohortResponseQueriesItem
+
+
+class ConstrueCohortResponse(UniversalBaseModel):
+    queries: typing.Optional[typing.List[ConstrueCohortResponseQueriesItem]] = None
+    sql: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Generated SQL query when `sql_syntax` is specified. Variables in curly braces need to be replaced with your actual table names.
+    """
+
+    cohort_description: typing_extensions.Annotated[typing.Optional[str], FieldMetadata(alias="cohortDescription")] = (
+        pydantic.Field(default=None)
+    )
+    """
+    Echo of the input text description for reference.
+    """
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/construe/types/construe_cohort_response_queries_item.py

@@ -0,0 +1,49 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+import typing_extensions
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+from ...core.serialization import FieldMetadata
+from .construe_cohort_response_queries_item_code_extract_results_item import (
+    ConstrueCohortResponseQueriesItemCodeExtractResultsItem,
+)
+
+
+class ConstrueCohortResponseQueriesItem(UniversalBaseModel):
+    resource: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    FHIR resource type (e.g., "Patient", "Condition").
+    """
+
+    search_params: typing_extensions.Annotated[typing.Optional[str], FieldMetadata(alias="searchParams")] = (
+        pydantic.Field(default=None)
+    )
+    """
+    FHIR search parameters.
+    """
+
+    exclude: typing.Optional[bool] = pydantic.Field(default=None)
+    """
+    Indicates if this is an exclusion criteria.
+    """
+
+    rationale: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    AI-generated explanation for the query component.
+    """
+
+    code_extract_results: typing_extensions.Annotated[
+        typing.Optional[typing.List[ConstrueCohortResponseQueriesItemCodeExtractResultsItem]],
+        FieldMetadata(alias="codeExtractResults"),
+    ] = None
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/construe/types/construe_cohort_response_queries_item_code_extract_results_item.py

@@ -0,0 +1,31 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+import typing_extensions
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+from ...core.serialization import FieldMetadata
+from .construe_cohort_response_queries_item_code_extract_results_item_codes_item import (
+    ConstrueCohortResponseQueriesItemCodeExtractResultsItemCodesItem,
+)
+
+
+class ConstrueCohortResponseQueriesItemCodeExtractResultsItem(UniversalBaseModel):
+    system_name: typing_extensions.Annotated[typing.Optional[str], FieldMetadata(alias="systemName")] = pydantic.Field(
+        default=None
+    )
+    """
+    Name of the coding system (e.g., "SNOMED_CT_US_LITE").
+    """
+
+    codes: typing.Optional[typing.List[ConstrueCohortResponseQueriesItemCodeExtractResultsItemCodesItem]] = None
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/construe/types/construe_cohort_response_queries_item_code_extract_results_item_codes_item.py

@@ -0,0 +1,32 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+
+
+class ConstrueCohortResponseQueriesItemCodeExtractResultsItemCodesItem(UniversalBaseModel):
+    code: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Medical code.
+    """
+
+    description: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Description of the medical code.
+    """
+
+    reason: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Reason for selecting the code.
+    """
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/construe/types/construe_upload_code_system_response.py

@@ -0,0 +1,19 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+
+
+class ConstrueUploadCodeSystemResponse(UniversalBaseModel):
+    status: typing.Optional[str] = None
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/construe/types/extract_codes_result.py

@@ -0,0 +1,22 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+from .extract_request_system import ExtractRequestSystem
+from .extracted_code_result import ExtractedCodeResult
+
+
+class ExtractCodesResult(UniversalBaseModel):
+    system: ExtractRequestSystem
+    codes: typing.List[ExtractedCodeResult]
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/construe/types/extract_request_config.py

@@ -0,0 +1,23 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+from .extract_request_config_chunking_method import ExtractRequestConfigChunkingMethod
+
+
+class ExtractRequestConfig(UniversalBaseModel):
+    chunking_method: typing.Optional[ExtractRequestConfigChunkingMethod] = None
+    max_codes_per_chunk: typing.Optional[int] = None
+    code_similarity_filter: typing.Optional[float] = None
+    include_rationale: typing.Optional[bool] = None
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/construe/types/extract_request_config_chunking_method.py

@@ -0,0 +1,5 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+ExtractRequestConfigChunkingMethod = typing.Union[typing.Literal["none", "sentence", "paragraph", "topics"], typing.Any]

phenoml/construe/types/extract_request_system.py

@@ -0,0 +1,37 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+
+
+class ExtractRequestSystem(UniversalBaseModel):
+    name: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Code system name. Can be a built-in system or a custom system name.
+    
+    Built-in systems:
+    * SNOMED_CT_US_LITE - version 20240901
+    * RXNORM - version 11042024
+    * ICD-10-CM - version 2025
+    * ICD-10-PCS - version 2025
+    * LOINC - version 2.78
+    
+    Custom systems:
+    * Any valid system name configured in your environment. Must have self-hosted construe module.
+    """
+
+    version: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Code system version. Must match the version available in your environment.
+    """
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/construe/types/extracted_code_result.py

@@ -0,0 +1,41 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+import typing_extensions
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+from ...core.serialization import FieldMetadata
+
+
+class ExtractedCodeResult(UniversalBaseModel):
+    code: str = pydantic.Field()
+    """
+    The extracted code
+    """
+
+    description: str = pydantic.Field()
+    """
+    Short description of the code
+    """
+
+    long_description: typing_extensions.Annotated[typing.Optional[str], FieldMetadata(alias="longDescription")] = (
+        pydantic.Field(default=None)
+    )
+    """
+    Long description of the code
+    """
+
+    rationale: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Explanation for why this code was extracted (if include_rationale is true)
+    """
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/construe/types/internal_server_error_body.py

@@ -0,0 +1,27 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+
+
+class InternalServerErrorBody(UniversalBaseModel):
+    status: typing.Optional[int] = pydantic.Field(default=None)
+    """
+    HTTP status code.
+    """
+
+    message: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Error message.
+    """
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/construe/types/unauthorized_error_body.py

@@ -0,0 +1,27 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+
+
+class UnauthorizedErrorBody(UniversalBaseModel):
+    status: typing.Optional[int] = pydantic.Field(default=None)
+    """
+    HTTP status code.
+    """
+
+    message: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Error message.
+    """
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/construe/types/upload_request_format.py

@@ -0,0 +1,5 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+UploadRequestFormat = typing.Union[typing.Literal["json", "csv"], typing.Any]

phenoml/core/__init__.py

@@ -0,0 +1,52 @@
+# This file was auto-generated by Fern from our API Definition.
+
+# isort: skip_file
+
+from .api_error import ApiError
+from .client_wrapper import AsyncClientWrapper, BaseClientWrapper, SyncClientWrapper
+from .datetime_utils import serialize_datetime
+from .file import File, convert_file_dict_to_httpx_tuples, with_content_type
+from .http_client import AsyncHttpClient, HttpClient
+from .http_response import AsyncHttpResponse, HttpResponse
+from .jsonable_encoder import jsonable_encoder
+from .pydantic_utilities import (
+    IS_PYDANTIC_V2,
+    UniversalBaseModel,
+    UniversalRootModel,
+    parse_obj_as,
+    universal_field_validator,
+    universal_root_validator,
+    update_forward_refs,
+)
+from .query_encoder import encode_query
+from .remove_none_from_dict import remove_none_from_dict
+from .request_options import RequestOptions
+from .serialization import FieldMetadata, convert_and_respect_annotation_metadata
+
+__all__ = [
+    "ApiError",
+    "AsyncClientWrapper",
+    "AsyncHttpClient",
+    "AsyncHttpResponse",
+    "BaseClientWrapper",
+    "FieldMetadata",
+    "File",
+    "HttpClient",
+    "HttpResponse",
+    "IS_PYDANTIC_V2",
+    "RequestOptions",
+    "SyncClientWrapper",
+    "UniversalBaseModel",
+    "UniversalRootModel",
+    "convert_and_respect_annotation_metadata",
+    "convert_file_dict_to_httpx_tuples",
+    "encode_query",
+    "jsonable_encoder",
+    "parse_obj_as",
+    "remove_none_from_dict",
+    "serialize_datetime",
+    "universal_field_validator",
+    "universal_root_validator",
+    "update_forward_refs",
+    "with_content_type",
+]

phenoml/core/api_error.py

@@ -0,0 +1,23 @@
+# This file was auto-generated by Fern from our API Definition.
+
+from typing import Any, Dict, Optional
+
+
+class ApiError(Exception):
+    headers: Optional[Dict[str, str]]
+    status_code: Optional[int]
+    body: Any
+
+    def __init__(
+        self,
+        *,
+        headers: Optional[Dict[str, str]] = None,
+        status_code: Optional[int] = None,
+        body: Any = None,
+    ) -> None:
+        self.headers = headers
+        self.status_code = status_code
+        self.body = body
+
+    def __str__(self) -> str:
+        return f"headers: {self.headers}, status_code: {self.status_code}, body: {self.body}"

phenoml/core/client_wrapper.py

@@ -0,0 +1,87 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import httpx
+from .http_client import AsyncHttpClient, HttpClient
+
+
+class BaseClientWrapper:
+    def __init__(
+        self,
+        *,
+        token: typing.Optional[typing.Union[str, typing.Callable[[], str]]] = None,
+        headers: typing.Optional[typing.Dict[str, str]] = None,
+        base_url: str,
+        timeout: typing.Optional[float] = None,
+    ):
+        self._token = token
+        self._headers = headers
+        self._base_url = base_url
+        self._timeout = timeout
+
+    def get_headers(self) -> typing.Dict[str, str]:
+        headers: typing.Dict[str, str] = {
+            "User-Agent": "phenoml/0.0.6",
+            "X-Fern-Language": "Python",
+            "X-Fern-SDK-Name": "phenoml",
+            "X-Fern-SDK-Version": "0.0.6",
+            **(self.get_custom_headers() or {}),
+        }
+        token = self._get_token()
+        if token is not None:
+            headers["Authorization"] = f"Bearer {token}"
+        return headers
+
+    def _get_token(self) -> typing.Optional[str]:
+        if isinstance(self._token, str) or self._token is None:
+            return self._token
+        else:
+            return self._token()
+
+    def get_custom_headers(self) -> typing.Optional[typing.Dict[str, str]]:
+        return self._headers
+
+    def get_base_url(self) -> str:
+        return self._base_url
+
+    def get_timeout(self) -> typing.Optional[float]:
+        return self._timeout
+
+
+class SyncClientWrapper(BaseClientWrapper):
+    def __init__(
+        self,
+        *,
+        token: typing.Optional[typing.Union[str, typing.Callable[[], str]]] = None,
+        headers: typing.Optional[typing.Dict[str, str]] = None,
+        base_url: str,
+        timeout: typing.Optional[float] = None,
+        httpx_client: httpx.Client,
+    ):
+        super().__init__(token=token, headers=headers, base_url=base_url, timeout=timeout)
+        self.httpx_client = HttpClient(
+            httpx_client=httpx_client,
+            base_headers=self.get_headers,
+            base_timeout=self.get_timeout,
+            base_url=self.get_base_url,
+        )
+
+
+class AsyncClientWrapper(BaseClientWrapper):
+    def __init__(
+        self,
+        *,
+        token: typing.Optional[typing.Union[str, typing.Callable[[], str]]] = None,
+        headers: typing.Optional[typing.Dict[str, str]] = None,
+        base_url: str,
+        timeout: typing.Optional[float] = None,
+        httpx_client: httpx.AsyncClient,
+    ):
+        super().__init__(token=token, headers=headers, base_url=base_url, timeout=timeout)
+        self.httpx_client = AsyncHttpClient(
+            httpx_client=httpx_client,
+            base_headers=self.get_headers,
+            base_timeout=self.get_timeout,
+            base_url=self.get_base_url,
+        )

phenoml/core/datetime_utils.py

@@ -0,0 +1,28 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import datetime as dt
+
+
+def serialize_datetime(v: dt.datetime) -> str:
+    """
+    Serialize a datetime including timezone info.
+
+    Uses the timezone info provided if present, otherwise uses the current runtime's timezone info.
+
+    UTC datetimes end in "Z" while all other timezones are represented as offset from UTC, e.g. +05:00.
+    """
+
+    def _serialize_zoned_datetime(v: dt.datetime) -> str:
+        if v.tzinfo is not None and v.tzinfo.tzname(None) == dt.timezone.utc.tzname(None):
+            # UTC is a special case where we use "Z" at the end instead of "+00:00"
+            return v.isoformat().replace("+00:00", "Z")
+        else:
+            # Delegate to the typical +/- offset format
+            return v.isoformat()
+
+    if v.tzinfo is not None:
+        return _serialize_zoned_datetime(v)
+    else:
+        local_tz = dt.datetime.now().astimezone().tzinfo
+        localized_dt = v.replace(tzinfo=local_tz)
+        return _serialize_zoned_datetime(localized_dt)